Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for...

Area of Science:

• Microbiology
• Genomics
• Food Science

Background:

• Microbiomes are crucial for health, environment, and food production.
• Complex microbiomes are challenging to study, but cheese rinds offer a tractable model system.
• Understanding microbial interactions in cheese rinds can provide insights into broader ecological principles.

Purpose of the Study:

• To comprehensively analyze the genomic potential and temporal dynamics of cheese rind microbial communities.
• To establish a reproducible model system for studying microbial interactions in a complex environment.
• To generate a genomic catalog and predict mobile genetic element associations within cheese rinds.

Main Methods:

• Longitudinal, multi-platform metagenomic sequencing of three ripening washed-rind cheeses.
• Whole-genome sequencing of isolated microbial community members.
• Development of a 16-member in vitro washed-rind cheese system for experimental validation.

Main Results:

• Highly reproducible microbial succession was observed across all cheeses studied.
• Closely related Psychrobacter species were found to coexist.
• Mobile genetic elements (plasmids, phages) and their potential hosts were identified.
• A phyla-spanning bacterial genomic catalog was generated.
• The feasibility of reconstructing the cheese rind microbiome in vitro was demonstrated.

Conclusions:

• The combination of metagenomic time-series data and an in vitro model provides a robust platform for investigating cheese rind microbiomes.
• This research offers a valuable resource for both computational and experimental studies of microbial dynamics and functions.
• The findings facilitate hypothesis generation and testing regarding the ecological roles of specific microbes and genes in complex environments.